Hey :) What about -pbc nojump -center ?
Cheers, Tsjerk On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/26/14, 12:30 PM, Eric Smoll wrote: > >> Hello GROMACS users, >> >> I have created an infinite liquid film system by building a slab of >> molecules in a 3D periodic unit cell where two dimensions of the film (x >> and y) extend out to the edge of the unit cell and one (z) does not. >> >> I found the slab drifts along the z-dimension during MD and I am trying to >> post-process the trajectories to anchor the slab in the center of the unit >> cell. >> >> "trjconv -pbc mol -center -boxcenter" works well for most trajectories >> *unless* the slab drifts so much that it comes in contact with the z >> boundary. When this occurs, "trjconv -pbc mol -center -boxcenter" anchors >> it in a different location. Any ideas how I can anchor the system to the >> center of the unit cell in this situation? >> >> > The -fit options should help here, either progressive or translation. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.